PEF is a database that is intended to be used as a silo, isolated from everything else. It comes with its own LCIA method that only fits to this database. This is thinking behind the EF (to create one database, with specific elementary flows). Other databases on Nexus don't fit to this database, but for the remaining databases, we try to map the flows to one reference flow system that is in turn recognised and used by the LCIA method pack we provide. There are some exceptions: The IO databases (eora / PSILCA; exiobase) have each an own flow nomenclature; GaBi databases (that we provide for maintenance or to those who have the license and want to use it in openLCA) have their own LCIA method.
It is possible, technically, to merge two LCIA methods of course; if you use an SQL script, that is not too much effort.
All the best,